2 Answers
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Not necessarily. There are indeed various halachos where there is a dispute whether they are Biblical or Rabbinic obligations. One example that I can think of, offhand, is tevilas kelim (immersing dishes), about which Pri Chadash (Yoreh De'ah 120:1) cites variant opinions as to its source.

The Gemarah in Sotah brings a Posuk as its source and many Rishonim learn it as an actual Torah source but Rambam maintains it is just an asmachtah, and really it is just like all other Birchos Hamitzvos. He is a daas yahid on this issue. It seems that the exact tradition whether it was midioraisa or not was not explicitly taught and the Rishonim on each side have their reasoning as to why they hold what they do. There are many instances of lost Mesorah which results in a later argument.